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commit: de8eb4ef90bedc116258edad0d769d7469dbc28c |
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Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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AuthorDate: Tue Mar 3 15:16:58 2015 +0000 |
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Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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CommitDate: Tue Mar 3 15:16:58 2015 +0000 |
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URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de8eb4ef |
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|
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IMport to CVS |
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|
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Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
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|
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sci-biology/bwa/bwa-0.7.12.ebuild | 34 -------------------------------- |
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sci-biology/bwa/files/bwa_Makefile.patch | 27 ------------------------- |
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sci-biology/bwa/metadata.xml | 5 ----- |
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3 files changed, 66 deletions(-) |
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|
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diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild |
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deleted file mode 100644 |
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index 62488f3..0000000 |
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--- a/sci-biology/bwa/bwa-0.7.12.ebuild |
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+++ /dev/null |
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@@ -1,34 +0,0 @@ |
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-# Copyright 1999-2015 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Header: $ |
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- |
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-EAPI=5 |
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- |
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-inherit eutils toolchain-funcs |
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- |
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-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" |
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-HOMEPAGE="http://bio-bwa.sourceforge.net/" |
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-SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" |
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- |
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-LICENSE="GPL-3" |
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-SLOT="0" |
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-IUSE="" |
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-KEYWORDS="~amd64 ~x86 ~x64-macos" |
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- |
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-PATCHES=( "${FILESDIR}"/${PN}_Makefile.patch ) |
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- |
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-src_prepare() { |
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- epatch ${PATCHES[@]} |
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- tc-export CC AR |
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-} |
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- |
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-src_install() { |
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- dobin bwa |
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- |
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- doman bwa.1 |
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- |
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- exeinto /usr/libexec/${PN} |
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- doexe qualfa2fq.pl xa2multi.pl |
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- |
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- dodoc NEWS.md README-alt.md README.md |
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-} |
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|
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diff --git a/sci-biology/bwa/files/bwa_Makefile.patch b/sci-biology/bwa/files/bwa_Makefile.patch |
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deleted file mode 100644 |
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index 406e9b0..0000000 |
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--- a/sci-biology/bwa/files/bwa_Makefile.patch |
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+++ /dev/null |
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@@ -1,27 +0,0 @@ |
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---- Makefile |
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-+++ Makefile |
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-@@ -1,8 +1,8 @@ |
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--CC= gcc |
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-+CC?= gcc |
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- #CC= clang --analyze |
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--CFLAGS= -g -Wall -Wno-unused-function -O2 |
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-+CFLAGS?= -g -Wall -Wno-unused-function -O2 |
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- WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS |
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--AR= ar |
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-+AR?= ar |
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- DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) |
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- LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o |
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- AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ |
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-@@ -26,10 +26,10 @@ |
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- all:$(PROG) |
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- |
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- bwa:libbwa.a $(AOBJS) main.o |
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-- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) |
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-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) |
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- |
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- bwamem-lite:libbwa.a example.o |
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-- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) |
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-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) |
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- |
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- libbwa.a:$(LOBJS) |
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- $(AR) -csru $@ $(LOBJS) |
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|
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diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml |
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deleted file mode 100644 |
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index f17a827..0000000 |
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--- a/sci-biology/bwa/metadata.xml |
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+++ /dev/null |
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@@ -1,5 +0,0 @@ |
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-<?xml version="1.0" encoding="UTF-8"?> |
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-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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-<pkgmetadata> |
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- <herd>sci-biology</herd> |
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-</pkgmetadata> |
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